Supplementary Information New genomic insights into “Entotheonella” symbionts in Theonella swinhoei: mixotrophy, anaerobic adaptation, resilience and interaction Fang Liu, Jinlong Li, Guofang Feng, Zhiyong Li Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China * Correspondence Zhiyong Li: Marine Biotechnology Laboratory, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People’s Republic of China E-mail:
[email protected]; Tel.: 86-21-34204036; Fax: 86-21-34205709
Supplementary scripts Metagenome binning using MetaBAT: Step 1: run MetaBAT with default settings (sensitive mode) runMetaBat.sh metagenome-assembly.fa metagenome-assembly.sorted.bam Step 2: run MetaBAT with specific mode in the same folder (the *.depth.txt, *.TNF, and *.distance were generated in step 1) metabat -i metagenome-assembly.fa -a metagenome-assembly.fa.depth.txt -o output-folder -specific -l -v -m 2000 --saveTNF saved-metagenome-assembly.fa.depth.txt.TNF -saveDistance saved-metagenome-assembly.fa.depth.txt.distance ani.rb. and hmm.essential.rb were executed in enveomics-GUI which didn't require any command lines. The missing essential genes indicated by hmm.essential.rb were re-checked in the RASTtk annotation of four draft genomes. Genome annotation based on RASTtk #Double click RASTtk.app and navigate to terminal window. Here we use v4.2 as an example to show the command lines #One could perform the annotation using RASTtk pipeline on RAST website as well rast-create-genome --scientific-name "Entotheonella sp." --genetic-code 11 --domain Bacteria --contigs v4.2.fa > 4.2.gto rast-call-features-rRNA-SEED < 4.2.gto > GTO.2 rast-call-features-tRNA-trnascan < GTO.2 > GTO.3 rast-call-features-repeat-region-SEED < GTO.3 > GTO.4 rast-call-features-selenoprotein < GTO.4 > GTO.5 rast-call-features-pyrrolysoprotein < GTO.5 > GTO.6 rast-call-features-crispr < GTO.6 > GTO.7 rast-call-features-CDS-prodigal < GTO.7 > GTO.8 rast-call-features-CDS-glimmer3 < GTO.8 > GTO.9 rast-call-features-ProtoCDS-kmer-v2 < GTO.9 > GTO.10 rast-call-features-ProtoCDS-kmer-v1 < GTO.10 > GTO.11 rast-annotate-proteins-kmer-v2 < GTO.11 > GTO.12 rast-annotate-proteins-kmer-v1 -H < GTO.12 > GTO.13 rast-annotate-proteins-similarity -H < GTO.13 > GTO.14 rast-resolve-overlapping-features < GTO.14 > GTO.15 rast-export-genome feature_data < GTO.15 > 4.2.table
Figure S1. KEGG mapping results of glycolysis (brown), TCA cycle (green), the pentose phosphate pathway (orange), and the oxidative phosphorylation (red) in “Entotheonella” genomes.
Table S1. Representative Eukaryotic-like proteins in “Entotheonella” Uniprot ID a Protein v4.2 TSY2 1D-myo-inositol 2-amino-2TPR D5UPJ5 deoxy-alpha-D278.5 235.3 glucopyranoside ligase W4LJP9 Predicted GTP-binding protein LRR W4MAU1 Predicted GTP-binding protein 1033.9 1021.9 M9WXW8 50.8 Ankyrin repeat domain protein ARP A0A0C2QBL3 Ankyrin 72.4
v4.3
TSY1
282.3
282.3
1282.3
1542.3
49.7
49.7
a. Eukaryotic-like protein sequences were downloaded from Uniprot database. BLASTP program was used to search the Eukaryotic-like proteins in query genomes (e-value < 10-5). The best blast hit and the bitscore of each query genome was showed.
Table S2. Distribution of genes related to secretion systems in “Entotheonella” v4.3 TSY1 v4.2 GspD + + + GspE + + + GspA + + + GspK + + + GspL + + + GspN + + + GspF + + + Gsp GspC + + + GspG + + + GspJ + + + GspI + + + GspB + + + GspM + + + GspH + + + TadA + + + TadC + + + rcpA + + + TadB + + + rcpC + + + Flp pilus assembly protein + + + TadZ + + + ATPase with chaperone activity + + + WCI TadZ/CpaE + + + TadD + + + CpaD + + + Von Willebrand factor type A domain protein + + + TadG + + + ATP-dependent helicase + + + TadV + + TadE + TadF + *ClpB protein + + + *ImpH/VasB + + + *ImpA + + + *ImpJ/VasE + + + T6SS *IcmF-related protein + + + *ImpG/VasA + + + *ImpC + + + *ImpB + + + *ImpI/VasC + + +
TSY2 + + + + + + + + + + + + + + + + + + + + + + + + + +
*ImpF * lipoprotein/VasD *dotU *VgrG protein *ImpD *Secreted protein Hcp Sigma-54 dependent transcriptional regulator Protein phosphatase ImpM ImpN VasI ImpE * Core elements of T6SS
+ + + + + + + + -
+ + + + + + + + -
+ + + + + + + + + +
+ + + + + + + + +
